Publi.bib

@article{Chen:2014,
  author={C.-P. Chen and H. Fushing and R. Atwill and P. Koehl},
  title={biDCG: A new method for discovering global features of DNA microarray data via an iterative re-clustering procedure},
  journal={PLoS One},
  volume={9},
  pages={e102445},
  year={2014},
}

@article{Fushing:2014,
  author={H. Fushing and C. Chen and S.H. Liu and P. Koehl},
  title={Bootstrapping on undirected binary networks via statistical mechanics},
  journal={J.\ Stat.\ Phys.},
  volume={156},
  pages={853--862},
  year={2014},
}

@article{Carlsen:2014,
  author={M. Carlsen and P. Koehl abd P. R{\o}gen},
  title={On the importance of the distance measures used to train and test knowledge-based potentials for proteins},
  journal={PLoS One},
  notes = {in press},
  year = {(in press, 2014)}
}

@article{Li:2014,
  author={J. Li and P. Koehl},
  title={3D representations of amino acids -- applications to protein sequence comparison and classification},
  journal={Comp.\ Struct.\ Bio.\ J.},
  notes = {in press},
  year = {(in press, 2014)}
}

@article{Francis:2014,
  author = {P. Francis-Lyon and P. Koehl},
  title = {Protein side-chain modeling with a protein-dependent optimized rotamer library},
  journal = {Proteins: Struct.\ Func.\ Bioinfo.},
  notes = {in press},
  year = {(in press, 2014)}
}

@article{Violetta:2014,
  author = {V. Weinreb and L. Li and S.N. Chandrasekaran and P. Koehl and M. Delarue and C.W. Carter},
  title = {Domain Motion Sensed by the D1 Switch, a Remote Dynamic Packing Motif},
  journal = {J.\ Biol.\ Chem.},
  volume = {289},
  pages = {4367--4376},
  year = {2014}
}

@article{Koehl:2014,
  author = {P. Koehl},
  title = {Mathematics’s Role in the Grand Challenge of Deciphering the Molecular Basis of Life},
  journal = {Frontiers in biomolecular sciences},
  notes = {in press},
  year = {(in press, 2014)}
}

@article{Xia:2014,
  author = {F. Xei and D. Tong and W. Lifeng and H. Dayong and C.H. Steven and P. Koehl and L. Lu},
  title = {Identifying essential pairwise interactions in elastic network model using the alpha shape
	theory},
  journal = {J.\ Comp.\ Chem.},
  notes = {in press},
  year = {(in press, 2014)}
}

@article{Koehl:2014b,
  author = {P. Koehl and J. Hass},
  title = {Automatic alignment of genus-zero surfaces},
  journal = {{IEEE} Trans.\ Pattern Anal.\ Mach.\ Intell.},
  volume = {36},
  pages = {466--478},
  year = {2014}
}

@article{Koehl:2014c,
  author = {P. Koehl and F. Poitevin and H. Orland and M. Delarue},
  title = {Modified {P}oisson {B}oltzmann equations for characterizing biomolecular solvation},
  journal = {J.\ Theo.\ Comp.\ Chem.},
  pages = {1440001},
  year = {2014}
}

@article{Weiss:2014,
  author = {D. R. Weiss and P. Koehl},
  title = {Morphing methods to visualize coarse-grained protein dynamics},
  journal = {Methods Mol.\ Biol.},
  volume = {1084},
  page = {271--282},
  year = {2014}
}

@article{Li:2013,
  author = {J. Li and P. Mach and P. Koehl},
  title = {Measuring the shapes of macromolecules and why it matters},
  journal = {Comp.\ Struct.\ Biotech.\ J.},
  volume = {8},
  pages = {e201309001},
  year = {2013}
}

@inproceedings{Tsui:2013,
  author = {A. Tsui and D. Fenton and P. Vuong and J. Hass and P. Koehl 
		and N. Amenta and D. Coeurjolly and C. DeCarli and 
		O. T. Carmichael},
  title = {Globally Optimal Cortical Surface Matching with Exact Landmark
               Correspondence},
  booktitle = {Proc. Information Processing in Medical Imaging, IPMI 2013},
  year = {2013},
  pages = {487--498}
}

@article{Babakasal:2013,
  author = {B. Babakasal and D. D. Gae and J. Li and J. C. Lagarias and P. Koehl and A.J. Fisher},
  title = {His74 conservation in the bilin reductase {PcyA} family reflects an important role in protein-substrate structure and dynamics},
  journal = {Biochim.\ Biophys.\ Acta},
  volume = {537},
  pages = {233--242},
  year = {2013}
}

@article{Mach:2013,
  author = {P. Mach and P. Koehl},
  title = {Capturing protein sequence-structure specificity using computational sequence design},
  journal = {Proteins: Struct.\ Func.\ Bioinfo.},
  volume = {81},
  pages = {1556--1570},
  year = {2013}
}

@article{Fushing:2013,
  author = {H. Fushing and H. Wang and K. VanderWaal and B. McCowan and P. Koehl},
  title = {Multi-scale clustering by building a robust and self correcting ultrametric topology on data points},
  journal = {PLoS One},
  volume = {8},
  pages = {e56259},
  year = {2013}
}

@article{Sauguet:2013,
  author = {L. Sauguet and F. Poitevin and S. Murail and G. Moraga and C. van Renterghem and A. W. Thompson and P. Koehl and P. J. Corringer and M. Baaden and M. Delarue},
  title = {Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels},
  journal = {EMBO J.},
  volume = {32},
  pages = {728--741},
  year = {2013}
}

@article{Smaoui:2013,
  author = {M. R. Smaoui and F. Poitevin and M. Delarue and P. Koehl and H. Orland and J. Waldisp\"{u}hl},
  title = {Computational assembly of polymorphic amyloid fibrils reveals stable aggregates},
  journal = {Biophys.\ J.},
  volume = {104},
  pages = {683--693},
  year = {2013}
}

@article{Koehl:2013b,
  author = {P. Koehl and P. R{\o}gen},
  title = {Extracting knowledge from protein structure geometry},
  journal = {Proteins: Struct.\ Func.\ Bioinfo.},
  volume = {81},
  pages = {841--851},
  year = {2013}
}

@article{Diluccio:2012,
  author = {E. DiLuccio and P. Koehl},
  title = {The {H}-factor as a novel quality metric for homology modeling},
  journal = {J.\ Clin.\ Bioinfo},
  volume = {2},
  pages = {18--26},
  year = {2012}
}

@article{Kang:2012,
  author = {E. Kang and P. Koehl},
  title = {Identifying alpha-helices in proteins using the contact map and morphological operations},
  journal = {J. Korean Inst.\ Next Gen. Comput.},
  volume = {8},
  pages = {75--86},
  year = {2012}
}

@article{Mach:2012,
  author = {P. Mach and P. Koehl},
  title = {An analytical method for computing atomic contact areas in biomolecules},
  journal = {J.\ Comp.\ Chem.},
  volume = {34},
  pages = {105--120},
  year = {2012}
}

@article{Koehl:2012,
  author = {P. Koehl},
  title = {Fast Recursive Computation of 3D Geometric Moments from Surface Meshes},
  journal = {{IEEE} Trans.\ Pattern Anal.\ Mach.\ Intell.},
  volume = {34},
  pages = {2158--2163},
  year = {2012}
}

@article{Gu:2012,
  author = {S. Gu and P. Koehl and J. Hass and N. Amenta},
  title = {Surface-histogram: A new shape descriptor for protein-protein docking},
  journal = {Proteins: Struct.\ Func.\ Bioinfo.},
  volume = {80},
  pages = {221--238},
  year = {2012}
}

@article{Miao:2011,
  author = {L. Miao and H. Qin and P. Koehl and J. Song},
  title = {Selective and specific ion binding on proteins at physiologically-relevant concentrations},
  journal = {{FEBS} Lett.},
  volume = {585},
  pages = {3126--3132},
  year = {2011}
}

@article{Koehl:2011,
  author = {P. Koehl and H. Orland and M. Delarue},
  title = {Adapting {P}oisson-{B}oltzmann to the self-consistent mean field theory: Application to protein side-chain modeling},
  journal = {J.\ Chem.\ Phys.},
  volume = {135},
  pages = {055104},
  year = {2011}
}

@article{Mach:2011,
  author = {P. Mach and P. Koehl},
  title = {Geometric measures of large biomolecules: Surface, volume, and pockets},
  journal = {J.\ Comp.\ Chem.},
  volume = {32},
  pages = {3023--3038},
  year = {2011}
}

@article{Hu:2011,
  author = {C. Hu and P. Koehl and N. Max},
  title = {{PackHelix}: A tool for helix-sheet packing during protein structure prediction},
  journal = {Proteins: Struct.\ Func.\ Bioinfo.},
  volume = {78},
  pages = {2828--2843},
  year = {2011}
}

@article{Poitevin:2011,
  author = {F. Poitevin and H. Orland and S. Doniach and P. Koehl and M. Delarue},
  title = {{AquaSAXS}: A web server for computation and fitting of {SAXS} profiles with a non-uniform hydration layer},
  journal = {Nucl.\ Acids.\ Res.},
  volume = {39},
  pages = {W184--W189},
  year = {2011}
}

@article{Shi:2011,
  author = {X. Shi and P. Koehl},
  title = {Adaptive skin meshes coarsening for biomolecular simulation},
  journal = {Comput.\ Aided Graph.\ Design},
  volume = {28},
  pages = {307--320},
  year = {2011}
}

@article{Diluccio:2011,
  author = {E. DiLuccio and P. Koehl},
  title = {A quality metric for homology modeling: the {H}-factor},
  journal = {{BMC} Bioinformatics},
  volume = {12},
  pages = {48},
  year = {2011}
}

@article{Shi:2011b,
  author = {X. Shi and P. Koehl},
  title = {Geometry and topology for modeling biomolecular surfaces},
  journal = {Far East J.\ Applied Math.},
  volume = {50},
  pages = {1--34},
  year = {2011}
}

@article{FrancisLyon:2010,
  author = {P. Francis-Lyon and S. Gu and J. Hass and N. Amenta and P. Koehl},
  title = {Sampling the conformation of protein surface residues for flexible protein docking},
  journal = {{BMC} Bioinformatics},
  volume = {11},
  pages = {575},
  year = {2010}
}

@article{Koehl:2010,
  author = {P. Koehl and M. Delarue},
  title = {{AQUASOL}: an efficient solver for the dipolar {P}oisson-{B}oltzmann-{L}angevin equation},
  journal = {J.\ Chem.\ Phys.},
  volume = {132},
  pages = {064101},
  year = {2010}
}

@article{Hu:2010,
  author = {C. Hu and P. Koehl},
  title = {Helix-sheet packing in proteins},
  journal = {Proteins: Struct.\ Func.\ Bioinfo.},
  volume = {78},
  pages = {1736--1747},
  year = {2010}
}

@article{Koehl:2009,
  author = {P. Koehl and H. Orland and M. Delarue},
  title = {Computing ion solvation free energies using the Dipolar {P}oisson Model},
  journal = {J.\ Phys.\ Chem.\ B.},
  volume = {113},
  pages = {5694--5697},
  year = {2009}
}

@article{Koehl:2009b,
  author = {P. Koehl and H. Orland and M. Delarue},
  title = {Beyond {P}oisson-{B}oltzmann: Modeling biomolecule-water and water-water interactions},
  journal = {Phys.\ Rev.\ Let.},
  volume = {102},
  pages = {087801},
  year = {2009}
}

@inproceedings{Shi:2009,
  author = {X. Shi and P. Koehl},
  title = {Adaptive surface meshes coarsening with guaranteed quality and topology},
  booktitle = {Proc.\ Comput. Graphics Inter.\ Conf.},
  pages = {53--61},
  year = {2009}
}

@article{Laowanapiban:2009,
  author = {P. Laowanapiban and M. Kapustina and C. Vonrhein and M. Delarue and P. Koehl and C. W. Carter Jr},
  title = {Independent saturation of three {TrpRS} subsites generates a partially assembled state similar to those observed in molecular simulations},
  journal = {Proc.\ Natl.\ Acad.\ Sci.\ (USA)},
  volume = {106},
  pages = {1790--1795},
  year = {2009}
}

@article{Azuara:2008,
  author = {A. Azuara and H. Orland and M. Bon and P. Koehl and M. Delarue},
  title = {Incorporating dipolar solvents with variable density in {P}oisson-{B}oltzmann electrostatics},
  journal = {Biophys.\ J.},
  volume = {95},
  pages = {5587--5605},
  year = {2008}
}

@article{Le:2008,
  author = {Q. Le and G. Pollastri and P. Koehl},
  title = {Structural alphabets for protein structure classification: a comparison study},
  journal = {JMB},
  volume = {387},
  pages = {431--450},
  year = {2008}
}

@article{Shi:2008,
  author = {X. Shi and P. Koehl},
  title = {The geometry behind numerical solvers of the {P}oisson-{B}oltzmann equation},
  journal = {Commun.\ Comput.\ Phys.},
  volume = {3},
  pages = {1032--1050},
  year = {2008}
}

@inproceedings{Gu:2007,
  author = {S. Gu and O. Poch and B. Hamann and P. Koehl},
  title = {A geometric representation of protein sequences},
  booktitle = {{IEEE} International Conf.\ Biol.\ Medicine},
  pages = {135--142},
  year = {2007}
}

@article{Chalmel:2007,
  author = {F. Chalmel and T. Leveillard and C. Jaillard and A. Lardenois and N. Berdugo and E. Morel and P. Koehl and G. Lambrou and A. Holmgren and J. A. Sahel and O. Poch},
  title = {Rod-derived cone viability factor-2 is a novel bifunctional thioredoxin like protein with therapeutic potential},
  journal = {{BMC} Molec. Biol.},
  volume = {8},
  pages = {74--85},
  year = {2007}
}

@article{Franklin:2007,
  author = {J. Franklin and P. Koehl and S. Doniach and M. Delarue},
  title = {MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse grained locally harmonic energy landscape},
  journal = {Nucl.\ Acids.\ Res.},
  volume = {35},
  pages = {V477--W482},
  year = {2007}
}

@article{McHale:2006,
  author = {L. McHale and X. Tan and P. Koehl and R. Michelmore},
  title = {Plant {NBS-LRR} proteins: adaptable guards},
  journal = {Genome Biology},
  volume = {7},
  pages = {212},
  year = {2006}
}

@article{Zomorodian:2006,
  author = {A. Zomorodian and L. Guibas and P. Koehl},
  title = {Geometric filtering of pairwise atomic interactions applied to the design of efficient statistical potentials},
  journal = {Comput.\ Aided Graph.\ Design},
  volume = {23},
  pages = {531--544},
  year = {2006}
}

@article{Lindahl:2006,
  author = {E. Lindahl and C. Azuara and P. Koehl and M. Delarue},
  title = {{NORMAnDRef:} Visualization, Deformation, and Refinement of Macromolecular Structures based on all-atom Normal Mode Analysis},
  journal = {Nucl.\ Acids.\ Res.},
  volume = {34},
  pages = {W52--W56},
  year = {2006}
}

@article{Azuara:2006,
  author = {C. Azuara and E. Lindahl and P. Koehl and H. Orland and M. Delarue},
  title = {{PDB{\_}Hydro.} Incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics},
  journal = {Nucl.\ Acids.\ Res.},
  volume = {34},
  pages = {W38--W42},
  year = {2006}
}

@article{Thompson:2005,
  author = {J. D. Thompson and P. Koehl and R. Ripp and O. Poch},
  title = {{BAliBASE 3.0:} Latest developments of the multiple sequence alignment benchmark},
  journal = {Proteins: Struct.\ Func.\ Genet.},
  volume = {61},
  pages = {127--136},
  year = {2005}
}

@article{Thompson:2005b,
  author = {J. D. Thompson and S. R. Holbrook and K. Katoh and P. Koehl and D. Moras and E. Westhof and O. Poch},
  title = {{MAO}: a multiple alignment ontology for nucleic acid and protein sequences},
  journal = {Nucl.\ Acids.\ Res.},
  volume = {33},
  pages = {4164--4171},
  year = {2005}
}

@article{Edelsbrunner:2005,
  author = {H. Edelsbrunner and P. Koehl},
  title = {The geometry of biomolecular solvation},
  journal = {{MSRI} Publications},
  volume = {52},
  pages = {243--275},
  year = {2005}
}

@article{Koehl:2005,
  author = {P. Koehl},
  title = {Relaxed specificity in aromatic prenyltransferases},
  journal = {Nature Chem.\ Biol.},
  volume = {1},
  pages = {71--72},
  year = {2005}
}

@article{Kolodny:2005,
  author = {R. Kolodny and L. Guibas and M. Levitt and P. Koehl},
  title = {Inverse kinematics in biology: the protein loop closure problem},
  journal = {Int.\ J.\ Robot.\ Res.},
  volume = {24},
  pages = {151--163},
  year = {2005}
}

@article{Kolodny:2005b,
  author = {R. Kolodny and P. Koehl and M. Levitt},
  title = {Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures},
  journal = {J.\ Mol.\ Biol.},
  volume = {346},
  pages = {1173--1188},
  year = {2005}
}

@article{Birck:2004,
  author = {C. Birck and L. Damian and C. Marty-Detraves and A. Lougarre and C. Shulze Briese and P. Koehl and A. Fournie and L. Paquereau and J. P. Samama},
  title = {A new lectin family with structure similarity to actinoporins revealed by the crystal structure of \textit{Xerocomus chrysenteron} Lectin {XCL}},
  journal = {J.\ Mol.\ Biol.},
  volume = 344,
  pages = {1409--1420},
  year = {2004}
}

@article{Bryant:2004,
  author = {R. Bryant and H. Edelsbrunner and P. Koehl and M. Levitt},
  title = {The weighted area derivative of a space filling diagram},
  journal = {Discrete Comput.\ Geom.},
  volume = {32},
  pages = {293--308},
  year = {2004}
}

@article{Chandonia:2004,
  author = {J. M. Chandonia and N. S. Walker and L. L. Conte and P. Koehl and M. Levitt and S. E. Brenner},
  title = {Astral compendium enhancements},
  journal = {Nucl.\ Acids.\ Res.},
  volume = {32},
  pages = {D189--D192},
  year = {2004}
}

@article{Edelsbrunner:2003,
  author = {H. Edelsbrunner and P. Koehl},
  title = {The weighted volume derivative of a space filling diagram},
  journal = {Proc.\ Natl.\ Acad.\ Sci.\ (USA)},
  volume = {100},
  pages = {2203--2208},
  year = {2003}
}

@article{Koehl:2002,
  author = {P. Koehl and M. Levitt},
  title = {Sequence variations within protein families are linearly related to structural variations},
  journal = {J.\ Mol.\ Biol.},
  volume = {323},
  pages = {551--562},
  year = {2002}
}

@article{Kolodny:2002,
  author = {R. Kolodny and P. Koehl and L. Guibas and M. Levitt},
  title = {Small libraries of protein fragments model native protein structures accurately},
  journal = {J.\ Mol.\ Biol.},
  volume = {323},
  pages = {297--307},
  year = {2002}
}

@article{Koehl:2002b,
  author = {P. Koehl and M. Levitt},
  title = {Protein topology and Stability define the space of allowed sequences},
  journal = {Proc.\ Natl.\ Acad.\ Sci.\ (USA)},
  volume = {99},
  pages = {1280--1285},
  year = {2002}
}

@article{Chandonia:2002,
  author = {J. M. Chandonia and N. S. Walker and L. L. Conte and P. Koehl and M. Levitt and S. E. Brenner},
  title = {Astral compendium enhancements},
  journal = {Nucl.\ Acids.\ Res.},
  volume = {30},
  pages = {260--263},
  year = {2002}
}

@article{Koehl:2002c,
  author = {P. Koehl and M. Levitt},
  title = {Improved recognition of native-like protein structures using a family of designed sequences},
  journal = {Proc.\ Natl.\ Acad.\ Sci.\ (USA)},
  volume = {99},
  pages = {691--696},
  year = {2002}
}

@article{Wedeking:2001,
  author = {J. E. Wedeking and C. B. Trame and M. Dorywalska and P. Koehl and T. M. Rasche and M. McKee and D. Fitzgerald and R. J. Collier and D. B. McKay},
  title = {Refined crystallographic structure of Pseudomonas aeruginosa exotoxin A and its implications for the molecular mechanism of toxicity},
  journal = {J.\ Mol.\ Biol.},
  volume = {314},
  pages = {823--837},
  year = {2001}
}

@article{Rabier:2001,
  author = {P. Rabier and B. Kieffer and P. Koehl and J. F. Lef{\`{e}}vre},
  title = {Fast measurements of heteronuclear relaxation: frequency domain analysis of {NMR} accordion spectroscopy},
  journal = {Mag.\ Res.\ Chem.},
  volume = {39},
  pages = {447--456},
  year = {2001}
}

@article{Samudrala:2000,
  author = {R. Samudrala and E. S. Huang and P. Koehl and M. Levitt},
  title = {Constructing side-chains on near native main chains for ab initio protein structure prediction},
  journal = {Prot.\ Eng.},
  volume = {13},
  pages = {453--457},
  year = {2000}
}

@article{Brenner:2000,
  author = {S. E. Brenner and P. Koehl and M. Levitt},
  title = {The {A}stral compendium for protein structure and sequence analysis},
  journal = {Nucl.\ Acids.\ Res.},
  volume = {28},
  pages = {254--256},
  year = {2000}
}

@article{Koehl:1999,
  author = {P. Koehl and M. Levitt},
  title = {De novo protein design. {I}. In search of stability and specificity},
  journal = {J.\ Mol.\ Biol.},
  volume = {293},
  pages = {1161--1181},
  year = {1999}
}

@article{Koehl:1999b,
  author = {P. Koehl and M. Levitt},
  title = {De novo protein design. {II}. Plasticity of protein sequences},
  journal = {J.\ Mol.\ Biol.},
  volume = {293},
  pages = {1182--1193},
  year = {1999}
}

@article{Koehl:1999c,
  author = {P. Koehl and M. Levitt},
  title = {Structure-based conformational preferences of amino acids},
  journal = {Proc.\ Natl.\ Acad.\ Sci.\ (USA)},
  volume = {96},
  pages = {12524--12529},
  year = {1999}
}

@article{Huang:1998,
  author = {E. S. Huang and P. Koehl and M. Levitt and R. V. Pappu and J. W. Ponder},
  title = {Accuracy of side-chain prediction upon near-native protein backbones generated by ab-initio folding methods},
  journal = {Proteins: Struct.\ Func.\ Genet.},
  volume = {33},
  pages = {204--217},
  year = {1998}
}

@article{Furuichi:1998,
  author = {E. Furuichi and P. Koehl},
  title = {Influence of protein structure database on the predictive power of statistical pair potentials},
  journal = {Proteins: Struct.\ Func.\ Genet.},
  volume = {31},
  pages = {139--149},
  year = {1998}
}

@article{Koehl:1998,
  author = {P. Koehl and M. Delarue},
  title = {Building protein lattice models using self consistent mean field theory},
  journal = {J.\ Chem.\ Phys.},
  volume = {108},
  pages = {9540--9549},
  year = {1998}
}

@article{Sunada:1996,
  author = {S. Sunada and N. Go and P. Koehl},
  title = {Calculation of {NMR} order parameters in proteins by normal mode analysis},
  journal = {J.\ Chem.\ Phys.},
  volume = {104},
  pages = {4768--4775},
  year = {1996}
}

@article{Koehl:1995,
  author = {P. Koehl and C. Ling and J. F. Lef{\`{e}}vre},
  title = {Automatic phase correction of {NMR} spectra: statistics and limits},
  journal = {J.\ Chim.\ Phys.},
  volume = {92},
  pages = {1929--1938},
  year = {1995}
}

@article{Delarue:1995,
  author = {M. Delarue and P. Koehl},
  title = {Atomic environment energies in proteins defined from statistics of accessible and contact surface areas},
  journal = {J.\ Mol.\ Biol.},
  volume = {249},
  pages = {675--690},
  year = {1995}
}

@article{Koehl:1995b,
  author = {P. Koehl and M. Delarue},
  title = {A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modeling},
  journal = {Nature Struct.\ Biol.},
  volume = {2},
  pages = {163--170},
  year = {1995}
}

@article{Mer:1994,
  author = {G. Mer and C. Kellenberger and P. Koehl and R. Stote and O. Sorokine and A. Van Dorsselaer and B. Luu and H. Hietter and J. F. Lef{\`{e}}vre},
  title = {Disulphide bridge pairing and solution structure by {1H NMR} of {PMPD2}, a 35 residue peptide isolated from \textit{Locusta migratoria}},
  journal = {Biochemistry},
  volume = {33},
  pages = {15397--15409},
  year = {1994}
}

@article{Koehl:1994,
  author = {P. Koehl and M. Delarue},
  title = {Polar and non-polar atomic environments in the protein core: implications for folding and binding},
  journal = {Proteins: Struct.\ Func.\ Genet.},
  volume = {20},
  pages = {264--278},
  year = {1994}
}

@article{Koehl:1994b,
  author = {P. Koehl and C. Ling and J. F. Lef{\`{e}}vre},
  title = {Oversampling improves linear prediction quantification of magnetic resonance spectral parameters},
  journal = {J.\ Chim.\ Phys.},
  volume = {91},
  pages = {595--606},
  year = {1994}
}

@article{Koehl:1994c,
  author = {P. Koehl and M. Delarue},
  title = {Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy},
  journal = {J.\ Mol.\ Biol.},
  volume = {239},
  pages = {249--275},
  year = {1994}
}

@article{Koehl:1994d,
  author = {P. Koehl and C. Ling and J. F. Lef{\`{e}}vre},
  title = {Linear prediction quantification of magnetic resonance spectral parameters: statistics and limits},
  journal = {J.\ Magn.\ Reson.},
  volume = {A109},
  pages = {32--40},
  year = {1994}
}

@article{Mohn:1994,
  author = {G. Mohn and P. Koehl and H. Budzikiewicz and J. F. Lef{\`{e}}vre},
  title = {Solution structure of pyoverdin {GM-II}},
  journal = {Biochemistry},
  volume = {33},
  pages = {2843--2851},
  year = {1994}
}

@article{Bersch:1993,
  author = {B. Bersch and P. Koehl and Y. Nakatani and G. Ourisson and A. Milon},
  title = {{1H} nuclear magnetic resonance determination of the membrane-bound conformation of Senktide, a highly selective neurokinin {B} agonist},
  journal = {J.\ Biol.\ NMR},
  volume = {3},
  pages = {91--112},
  year = {1993}
}

@article{Kieffer:1993,
  author = {B. Kieffer and P. Koehl and S. Plaue and J. F. Lef{\`{e}}vre},
  title = {Structural and dynamic studies of two antigenic loops from Haemagglutinin: a relaxation matrix approach},
  journal = {J.\ Biol.\ NMR},
  volume = {3},
  pages = {91--112},
  year = {1993}
}

@article{Kieffer:1992,
  author = {B. Kieffer and P. Koehl and J. F. Lef{\`{e}}vre},
  title = {Modeling the dynamic of an antigenic peptide using {NMR} data},
  journal = {Biochimie},
  volume = {74},
  pages = {815--824},
  year = {1992}
}

@article{Koehl:1992,
  author = {P. Koehl and B. Kieffer and J. F. Lef{\`{e}}vre},
  title = {Computer-assisted assignment of biological macromolecule {NMR} spectra},
  journal = {J.\ Chim.\ Phys.},
  volume = {89},
  pages = {135--146},
  year = {1992}
}

@article{Koehl:1992b,
  author = {P. Koehl and J. F. Lef{\`{e}}vre and O. Jardetzky},
  title = {Computing the geometry of a molecule in dihedral angle space using {NMR}-derived constraints: a new algorithm based on optimal filtering},
  journal = {J.\ Mol.\ Biol.},
  volume = {223},
  pages = {299--315},
  year = {1992}
}

@article{Koehl:1990,
  author = {P. Koehl and J. F. Lef{\`{e}}vre},
  title = {The relaxation matrix reconstructed from an incomplete set of {2D-NOE} data: Statistics and Limits},
  journal = {Bull.\ Magn.\ Reson.},
  volume = {12},
  pages = {23--29},
  year = {1990}
}

@article{Koehl:1990b,
  author = {P. Koehl and J. F. Lef{\`{e}}vre},
  title = {The reconstruction of the relaxation matrix from an incomplete set of nuclear {O}verhauser effects},
  journal = {J.\ Magn.\ Reson.},
  volume = {87},
  pages = {565--583},
  year = {1990}
}

@article{Koehl:1989,
  author = {P. Koehl and P. Valladier and J. F. Lef{\`{e}}vre and R. P. P. Fuchs},
  title = {Strong structural effect of the position of a single acetylaminofluorene adduct within a mutation hot spot},
  journal = {Nucl.\ Acids.\ Res.},
  volume = {17},
  pages = {9531--9541},
  year = {1989}
}

@article{Burnouf:1989,
  author = {D. Burnouf and P. Koehl and R. P. P. Fuchs},
  title = {Single adduct mutagenesis : Strong effect of the position of a single acetylaminofluorene adduct within a mutation hot spot},
  journal = {Proc.\ Natl.\ Acad.\ Sci.\ (USA)},
  volume = {86},
  pages = {4147--4151},
  year = {1989}
}

@article{Koehl:1989b,
  author = {P. Koehl and D. Burnouf and R. P. P. Fuchs},
  title = {Construction of plasmids containing a unique acetylaminofluorene adduct located within a mutation hot spot: A new probe for frameshift mutagenesis},
  journal = {J.\ Mol.\ Biol.},
  volume = {207},
  pages = {355--364},
  year = {1989}
}

@article{Chatterjee:1986,
  author = {A. Chatterjee and P. Koehl and J. L. Magee},
  title = {Theoretical consideration of the chemical pathways for radiation-induced strand breaks},
  journal = {Adv.\ Space Res.},
  volume = {6},
  pages = {97--105},
  year = {1986}
}

@incollection{Koehl:2010b,
  author = {P. Koehl},
  title = {Protein Structure Prediction},
  booktitle = {Biomolecular applications of Biophysics},
  editor = {T. Jue},
  pages = {1--34},
  publisher = {Humana press},
  address = {New York, NY},
  year = {2010}
}

@incollection{Koehl:2009c,
  author = {P. Koehl},
  title = {Molecular force fields},
  booktitle = {Protein engineering and design},
  editor = {S. Park and J. Cochran},
  pages = {255--277},
  publisher = {CRC Press},
  address = {Boca Raton, Fl},
  year = {2009}
}

@inproceedings{Koehl:2009d,
  author = {P. Koehl and H. Orland and M. Delarue},
  title = {Solvation of Ion Pairs: The {P}oisson-{L}angevin Model},
  booktitle = {Proc.\ International Conf.\ Applied Phys.\ Math.},
  pages = {917--923},
  year = {2009}
}

@inproceedings{Natarajan:2008,
  author = {V. Natarajan and P. Koehl and Y. Wang and B. Hamann},
  title = {Visual analysis of biomolecular surfaces},
  booktitle = {Visualization in Medicine and Life Sciences},
  pages = {237--255},
  year = {2008}
}

@article{Koehl:2006,
  title = {Protein Structure Classification},
  author = {P. Koehl},
  journal = {Rev.\ Comput.\ Chem.},
  volume = {22},
  pages = {1--56},
  year = {2006}
}

@article{Koehl:2006b,
  author = {P. Koehl},
  title = {Electrostatics calculations: latest methodological advances},
  journal = {Curr.\ Opin.\ Struct.\ Biol.},
  volume = {16},
  pages = {142--151},
  year = {2006}
}

@article{Agarwal:2002,
  author = {P. Agarwal and L. Guibas and H. Edelsbrunner and J. Erickson and M. Isard and S. Har-Paled and J. Hershberger and C. Jensen and L. Kavraki and P. Koehl and M. Lin and D. Manocha and D. Metaxas and B. Mirtich and D. Mount and S. Muthukrishnan and D. Pai and E. Sacks and J. Snoeyink and S. Suri and O. Wolfson},
  title = {Algorithmic issues in modeling motion},
  journal = {ACM Computing surveys},
  volume = {34},
  pages = {550--572},
  year = {2002}
}

@incollection{Koehl:2002d,
  author = {P. Koehl},
  title = {Recent progress in computational protein design},
  booktitle = {Protein folding, stability, and design},
  editor = {M. Gromiha and S. Selvaraj},
  publisher = {Research Signpost},
  address = {Trivvendrum, India},
  pages = {307--324},
  year = {2002}
}

@incollection{Koehl:2001b,
  author = {P. Koehl and M. Levitt},
  title = {De novo protein design},
  editor = {O. Jardetzky and M. D. Finucane},
  booktitle = {{NATO} ASI Series vol. 315},
  pages = {57--75},
  publisher = {Plenum press},
  address = {New York, NY},
  year = {2001}
}

@article{Koehl:2001,
  author = {P. Koehl},
  title = {Protein structure similarities},
  journal = {Curr.\ Opin.\ Struct.\ Biol.},
  volume = {11},
  pages = {348--353},
  year = {2001}
}

@article{Koehl:1999d,
  author = {P. Koehl},
  title = {Linear prediction spectral analysis of {NMR} data},
  journal = {Progress in NMR spectroscopy},
  volume = {34},
  pages = {257--299},
  year = {1999}
}

@article{Koehl:1999e,
  author = {P. Koehl and M. Levitt},
  title = {A brighter future for protein structure prediction},
  journal = {Nature Struct.\ Biol.},
  volume = {6},
  pages = {108--111},
  year = {1999}
}

@article{Koehl:1999f,
  author = {P. Koehl and M. Levitt},
  title = {Theory and simulation: Can theory challenge experiment?},
  journal = {Curr.\ Opin.\ Struct.\ Biol.},
  volume = {9},
  pages = {155--156},
  year = {1999}
}

@inproceedings{Koehl:1997,
  author = {P. Koehl and M. Delarue},
  title = {The native sequence determines sidechain packing in a protein,
but does optimal sidechain packing determine the native sequence?},
  booktitle = {Proc.\ Pacific Symp.\ Biocomputing},
  pages = {198--209},
  year = {1997}
}

@inproceedings{Koehl:1997b,
  author = {M. Delarue and P. Koehl},
  title = {The inverse protein folding problem: self consistent mean field optimization of a structure specific mutation matrix},
  booktitle = {Proc.\ Pacific Symp.\ Biocomputing},
  pages = {109--121},
  year = {1997}
}

@article{Koehl:1996,
  author = {P. Koehl and M. Delarue},
  title = {Mean field minimization methods for biological macromolecules},
  journal = {Curr.\ Opin.\ Struct.\ Biol.},
  volume = {2},
  pages = {222--226},
  year = {1996}
}

@incollection{Koehl:1995c,
  author = {P. Koehl and J. F. Lef{\`{e}}vre},
  title = {Relaxation Matrix Refinement: Nucleic Acids},
  booktitle = {Encyclopedia of Nuclear Magnetic Resonance},
  editor = {D. M. Grant and R. K. Harris},
  publisher = {Wiley},
  address = {Chichester, England},
  year = {1995}
}

@incollection{Koehl:1995d,
  author = {P. Koehl and M. Delarue},
  title = {Modeling side-chain conformation in proteins: a self consistent mean field approach},
  booktitle = {Protein Engineering and Complementary Technologies},
  editor = {M. Geisow and R. Epton},
  publisher = {Mayflower Worldwide Ltd},
  address = {Birmingham, England},
  pages = {31--34},
  year = {1995}
}

@incollection{Koehl:1991,
  author = {P. Koehl and D. Burnouf and R. P. P. Fuchs},
  title = {Mutagenesis induced by a single acetylaminofluorene adduct within the NarI site is position dependent},
  booktitle = {Nitroarenes: Occurrence, Metabolism and Biological Impact},
  editor = {P. C. Howard and S. S. Hecht and F. A. Beland},
  publisher = {Plenum Press},
  address = {New York, NY},
  pages = {105--112},
  year = {1991}
}

@incollection{Koehl:1990c,
  author = {P. Koehl and B. Kieffer and J. F. Lef{\`{e}}vre},
  title = {The dynamics of oligonucleotides and peptides determined by proton {NMR}},
  editor = {O. Jardetzky},
  booktitle = {{NATO} ASI Series vol. 183},
  pages = {139--154},
  publisher = {Plenum press},
  address = {New York, NY},
  year = {1990}
}

@incollection{Koehl:1990d,
  author = {D. Burnouf and P. Koehl and R. P. P. Fuchs},
  title = {Position of a single acetylaminofluorene adduct within a mutational hot spot is critical for the related mutagenic event},
  booktitle = {Antimutagenesis and Anticarcinogenesis Mechanisms {II}},
  editor = {Y. Kuroda and D. M. Shankel and M. D. Waters},
  publisher = {Plenum Press},
  address = {New York, NY},
  pages = {277--288},
  year = {1990}
}